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We assess the impact of QSOs on the high redshift (z > 4) Intergalactic Medium using Monte Carlo realisations of QSO populations and the HeIII regions they generate, applied to the Sherwood-Relics simulations, allowing for uncertainties in the QSO luminosity function, its evolution, and QSO spectra and ages. While QSO luminosity functions based on optical-infrared selection are unable to reproduce the broadening HI Lyman-alpha optical depth distributions at z > 5, much broader distributions are found for the higher numbers of QSOs based on x-ray selection, suggesting a large QSO contribution to the ultra-violet background at z > 5 may offer an alternative to late reionization models to account for the broad HI Lyman-alpha optical depth distributions. Realisations using QSOs based on the higher QSO counts also much better recover the measured pixel flux auto-correlation function at z > 5. The HeIII regions from QSO sources according to both types of luminosity function suppress the pixel flux power spectrum on small scales, k > 0.02 s/km, while enhancing it on larger, both by amounts of up to tens of percent at z > 4, with the magnitude increasing with the intergalactic HeIII filling factor and the boost in temperature within the HeIII regions., Comment: Accepted for publication in MNRAS; 10 pages, 33 figures

The scattering of Ly$\alpha$ photons from the first radiating sources in the Universe plays a pivotal role in 21-cm radio detections of Cosmic Dawn and the Epoch of Reionization through the Wouthuysen-Field effect. New data from JWST show the Ly$\alpha$ photon scattering rate exceeds that required to decouple the intergalactic hydrogen spin temperature from that of the Cosmic Microwave Background up to $z\sim14$ and render the neutral hydrogen visible over the main redshift range expected for the Epoch of Reionization., Comment: Published in the Research Notes of the American Astronomical Society; 3 pages, 1 figure

We compare numerical methods for solving the radiative transfer equation in the context of the photoionization of intergalactic gaseous hydrogen and helium by a central radiating source. Direct integration of the radiative transfer equation and solutions using photon packets are examined, both for solutions to the time-dependent radiative transfer equation and in the infinite-speed-of-light approximation. The photon packet schemes are found to be more generally computationally efficient than a direct integration scheme. Whilst all codes accurately describe the growth rate of hydrogen and helium ionization zones, it is shown that a fully time-dependent method is required to capture the gas temperature and ionization structure in the near zone of a source when an ionization front expands at a speed close to the speed of light. Applied to Quasi-Stellar Objects in the Epoch of Reionization (EoR), temperature differences as high as $5\times10^4$ K result in the near-zone for solutions of the time-dependent radiative transfer equation compared with solutions in the infinite-speed-of-light approximation. Smaller temperature differences are found following the nearly full photoionization of helium in gas in which the hydrogen was already ionized and the helium was singly ionized. Variations found in the temperature and ionization structure far from the source, where the gas is predominantly neutral, may affect some predictions for 21-cm EoR experiments., Comment: 19 pages, 24 figures, submitted to MNRAS

We investigate the possible influence of fluctuations in the metagalactic photoionizing ultra-violet background (UVBG) on the clustering of Ly$\alpha$-emitting galaxies through the modulation of the ionization level of the gas surrounding the systems. At redshifts $z > 5$, even when assuming the reionization of the intergalactic medium has completed, the fluctuations are sufficiently large that they may non-negligibly enhance, and possibly even dominate, the angular correlation function on scales up to a few hundred arcsecs. Whilst a comparison with observations at $z \sim 5.7$ is statistically consistent with no influence of UVBG fluctuations, allowing for the fluctuations opens up the range of acceptable models to include those with relatively low bias factors for the Ly$\alpha$-emitting galaxies. In this case, the evolution in the bias factor of Ly$\alpha$-emitters over the approximate redshift range $3 < z < 7$ corresponds to a nearly constant halo mass for Ly$\alpha$-emitting galaxies of $\sim 10^{10.5}\,M_\odot$., Comment: 11 pages, 8 figures; accepted for publication in MNRAS

We present the Sherwood-Relics simulations, a new suite of large cosmological hydrodynamical simulations aimed at modelling the intergalactic medium (IGM) during and after the cosmic reionization of hydrogen. The suite consists of over 200 simulations that cover a wide range of astrophysical and cosmological parameters. It also includes simulations that use a new lightweight hybrid scheme for treating radiative transfer effects. This scheme follows the spatial variations in the ionizing radiation field, as well as the associated fluctuations in IGM temperature and pressure smoothing. It is computationally much cheaper than full radiation hydrodynamics simulations and circumvents the difficult task of calibrating a galaxy formation model to observational constraints on cosmic reionization. Using this hybrid technique, we study the spatial fluctuations in IGM properties that are seeded by patchy cosmic reionization. We investigate the relevant physical processes and assess their impact on the z > 4 Lyman-alpha forest. Our main findings are: (i) Consistent with previous studies patchy reionization causes large scale temperature fluctuations that persist well after the end of reionization, (ii) these increase the Lyman-alpha forest flux power spectrum on large scales, and (iii) result in a spatially varying pressure smoothing that correlates well with the local reionization redshift. (iv) Structures evaporated or puffed up by photoheating cause notable features in the Lyman-alpha forest, such as flat-bottom or double-dip absorption profiles., Comment: Version accepted for publication in MNRAS, some discussions added, data added to Fig. 8. 24 pages, 15 figures. Images and movies may be viewed at https://www.nottingham.ac.uk/astronomy/sherwood-relics/

Direct-collapse black holes (DCBHs) forming at $z \sim$ 20 are currently the leading candidates for the seeds of the first quasars, over 200 of which have now been found at $z >$ 6. Recent studies suggest that DCBHs could be detected in the near infrared by the James Webb Space Telescope, Euclid, and the Roman Space Telescope. However, new radio telescopes with unprecedented sensitivities such as the Square Kilometer Array (SKA) and the Next-Generation Very Large Array (ngVLA) may open another window on the properties of DCBHs in the coming decade. Here we estimate the radio flux from DCBHs at birth at $z =$ 8 - 20 with several fundamental planes of black hole accretion. We find that they could be detected at $z \sim$ 8 by the SKA-FIN all-sky survey. Furthermore, SKA and ngVLA could discover 10$^6$ - 10$^7$ $M_{\odot}$ BHs out to $z \sim$ 20, probing the formation pathways of the first quasars in the Universe., Comment: 6 pages. 4 figures, accepted by ApJL

Observations at intermediate redshifts reveal the presence of numerous, compact, weak MgII absorbers with near to super-solar metallicities, often surrounded by more extended regions that produce CIV and/or OVI absorption in the circumgalactic medium at large impact parameters from luminous galaxies. Their origin and nature remains unclear. We hypothesize that undetected, satellite dwarf galaxies are responsible for producing some of these weak MgII absorbers. We test our hypothesis using gas dynamical simulations of galactic outflows from a dwarf satellite galaxy with a halo mass of $5\times10^{9}$ M$_{\odot}$, which could form in a larger $L^{*}$ halo at z=2, to study the gas interaction in the halo. We find that thin, filamentary, weak MgII absorbers are produced in two stages: 1) when shocked core collapse supernova (SNII) enriched gas descending in a galactic fountain gets shock compressed by upward flows driven by subsequent SNIIs and cools (phase 1), and later, 2) during an outflow driven by Type Ia supernovae that shocks and sweeps up pervasive SNII enriched gas, which then cools (phase 2). The width of the filaments and fragments are $\lesssim~100$ pc, and the smallest ones cannot be resolved at 12.8 pc resolution. The MgII absorbers in our simulations are continuously generated for >150 Myr by shocks and cooling, though each cloud survives for only ~60 Myr. Their metallicity is 10-20% solar metallicity and column density is $<10^{12}$ cm$^{-2}$. They are also surrounded by larger (0.5-1 kpc) CIV absorbers that seem to survive longer. In addition, larger-scale (>1 kpc) CIV and OVI clouds are produced in both expanding and shocked SNII enriched gas which is photoionized by the UV metagalactic radiation at intermediate redshift. Our simulation highlights the possibility of dwarf galactic outflows producing highly enriched multiphase gas., Comment: 21 pages, 16 figures

Allowing for enhanced Ly$\alpha$ photon line emission from Population III dominated stellar systems in the first forming galaxies, we show the 21-cm cosmic dawn signal at $10

We interpret observations of intergalactic low ionisation metal absorption systems at redshifts z $\gtrsim$5 in terms of pressure-confined clouds. We find clouds confined by the expected pressure of galactic haloes with masses $11<\log M_h/h^{-1}M_\odot<12$ provide a good description of the column density ratios between low ionisation metal absorbers. Some of the ratios, however, require extending conventional radiative transfer models of irradiated slabs to spherical (or cylindrical) clouds to allow for lines of sight passing outside the cores of the clouds. Moderate depletion of silicon onto dust grains is also indicated in some systems. The chemical abundances inferred span the range between solar and massive-star dominated stellar populations as may arise in starburst galaxies. The typical HI column densities matching the data correspond to Damped Lyman-$\alpha$ Absorbers (DLAs) or sub-DLAs, with sizes of 40 pc to 3 kpc, gas masses $3.5<\log M_c/M_\odot<8$ and metallicites $0.001-0.01Z_\odot$. Such systems continue to pose a challenge for galaxy-scale numerical simulations to reproduce., Comment: 19 pages, 10 figures, 12 Tables, submitted to MNRAS, comments welcome

The leading contenders for the seeds of the first quasars are direct collapse black holes (DCBHs) formed during catastrophic baryon collapse in atomically-cooled halos at $z \sim$ 20. The discovery of the Ly$\alpha$ emitter CR7 at $z =$ 6.6 was initially held to be the first detection of a DCBH, although this interpretation has since been challenged on the grounds of Spitzer IRAC and Very Large Telescope X-Shooter data. Here we determine if radio flux from a DCBH in CR7 could be detected and discriminated from competing sources of radio emission in the halo such as young supernovae and H II regions. We find that a DCBH would emit a flux of 10 - 200 nJy at 1.0 GHz, far greater than the sub-nJy signal expected for young supernovae but on par with continuum emission from star-forming regions. However, radio emission from a DCBH in CR7 could be distinguished from free-free emission from H II regions by its spectral evolution with frequency and could be detected by the Square Kilometer Array in the coming decade., Comment: 4 pages, 2 figures, accepted by ApJL

Under the assumption that galaxies and Quasi-Stellar Objects (QSOs) dominate the metagalactic ultra-violet (UV) background, it is shown that at high redshifts fluctuations in the UV background are dominated by QSO shot noise and have an auto-correlation length of a few to several comoving Mpcs, depending on the bright end of the QSO luminosity function. The correlations create long range spatial coherence in the neutral hydrogen fraction. Using a semi-analytic model, it is demonstrated that the coherence may account for the broad distribution in effective optical depths measured in the Ly$\alpha$ forest spectra of background QSOs, for line-of-sight segments of comoving length $50h^{-1}$ Mpc at redshifts $5

Spatial fluctuations in ultraviolet backgrounds can subtly modulate the distribution of extragalactic sources, a potential signal and systematic for large-scale structure surveys. While this modulation has been shown to be significant for 3D Ly alpha forest surveys, its relevance for other large-scale structure probes has been hardly explored, despite being the only astrophysical process that likely can affect clustering measurements on the scales of >~Mpc. We estimate that the background fluctuations, modulating the amount of H I, have a fractional effect of (0.03-0.3) x (k/[10^-2 Mpc^-1])^-1 on the power spectrum of 21 cm intensity maps at z = 1-3. We find a smaller effect for H alpha and Ly alpha intensity mapping surveys of (0.001-0.1) x (k/[10^-2 Mpc^-1])-1 and even smaller effect for more traditional surveys that correlate the positions of individual H alpha or Ly alpha emitters. We also estimate the effect of backgrounds on low-redshift galaxy surveys in general based on a simple model in which background fluctuations modulate the rate halo gas cools, modulating star formation: We estimate a maximum fractional effect on the power of ~0.01 (k/[10-2 Mpc-1])-1 at z = 1. We compare sizes of these imprints to cosmological parameter benchmarks for the next generation of redshift surveys: We find that ionizing backgrounds could result in a bias on the squeezed triangle non-Gaussianity parameter fNL that can be larger than unity for power spectrum measurements with a SPHEREx-like galaxy survey, and typical values of intensity bias. Marginalizing over a shape of the form k-1PL, where PL is the linear matter power spectrum, removes much of this bias at the cost of ~ 40% larger statistical errors., Comment: 13 pages, 8 figures, published in MNRAS

We present a formalism for computing time-dependent fluctuations in the cosmological photoionizing radiation background, extending background fluctuations models beyond the steady-state approximation. We apply this formalism to estimate fluctuations in the HI LyA flux redshift space power spectrum and its spatial correlation function at redshifts 2

The diffuse soft X-ray emissivity from galactic winds is computed during the Epoch of Reionization (EoR). We consider two analytic models, a pressure-driven wind and a superbubble model, and a 3D cosmological simulation including gas dynamics from the First Billion Years (FiBY) project. The analytic models are normalized to match the diffuse X-ray emissivity of star-forming galaxies in the nearby Universe. The cosmological simulation uses physically motivated star formation and wind prescriptions, and includes radiative transfer corrections. The models and the simulation all are found to produce sufficient heating of the Intergalactic Medium to be detectable by current and planned radio facilities through 21 cm measurements during the EoR. While the analytic models predict a 21 cm emission signal relative to the Cosmic Microwave Background sets in by $z_{\rm trans} \simeq 8 - 10$, the predicted signal in the FiBY simulation remains in absorption until reionization completes. The 21 cm absorption differential brightness temperature reaches a minimum of $\Delta T \simeq -130$ to $-200$ mK, depending on model. Allowing for additional heat from high mass X-ray binaries pushes the transition to emission to $z_{\rm trans} \simeq 10 - 12$, with shallower absorption signatures having a minimum of $\Delta T \simeq -110$ to $-140$ mK. The 21 cm signal may be a means of distinguishing between the wind models, with the superbubble model favouring earlier reheating. While an early transition to emission may indicate X-ray binaries dominate the reheating, a transition to emission as early as $z_{\rm trans} > 12$ would suggest the presence of additional heat sources., Comment: 16 pages. This is a pre-copyedited, author-produced PDF of an article accepted for publication in MNRAS following peer review. The version of record, MNRAS, 2017, volume 471, issue 3, is available online at: https://academic.oup.com/mnras/article/471/3/3632/4002694/Galactic-wind-X-ray-heating-of-the-intergalactic

Modern theories of galaxy formation predict that galaxies impact on their gaseous surroundings, playing the fundamental role of regulating the amount of gas converted into stars. While star-forming galaxies are believed to provide feedback through galactic winds, Quasi-Stellar Objects (QSOs) are believed instead to provide feedback through the heat generated by accretion onto a central supermassive black hole. A quantitative difference in the impact of feedback on the gaseous environments of star-forming galaxies and QSOs has not been established through direct observations. Using the Sherwood cosmological simulations, we demonstrate that measurements of neutral hydrogen in the vicinity of star-forming galaxies and QSOs during the era of peak galaxy formation show excess LyA absorption extending up to comoving radii of about 150 kpc for star-forming galaxies and 300 - 700 kpc for QSOs. Simulations including supernovae-driven winds with the wind velocity scaling like the escape velocity of the halo account for the absorption around star-forming galaxies but not QSOs., Comment: 11 pages, 10 figures; to appear in MNRAS

We present a detailed analysis of the ionization and thermal structure of the intergalactic medium (IGM) around a high-redshift QSO using a large suite of cosmological, multi-frequency radiative transfer (RT) simulations, exploring the contribution from galaxies as well as the QSO, and the effect of X-rays and secondary ionization. We show that in high-z QSO environments both the central QSO and the surrounding galaxies concertedly control the reionization morphology of hydrogen and helium and have a non-linear impact on the thermal structure of the IGM. A QSO imprints a distinctive morphology on H II regions if its total ionizing photon budget exceeds that of the surrounding galaxies since the onset of hydrogen reionization; otherwise, the morphology shows little difference from that of H II regions produced only by galaxies. In addition, the spectral shape of the collective radiation field from galaxies and QSOs controls the thickness of the I-fronts. While a UV-obscured QSO can broaden the I-front, the contribution from other UV sources, either galaxies or unobscured QSO, is sufficient to maintain a sharp I-front. X-rays photons from the QSO are responsible for a prominent extended tail of partial ionization ahead of the I-front. QSOs leave a unique imprint on the morphology of He II / He III regions. We suggest that, while the physical state of the IGM is modified by QSOs, the most direct test to understand the role of galaxies and QSOs during reionization is to perform galaxy surveys in a region of sky imaged by 21 cm tomography., Comment: 19 pages, 22 figures, submitted

We introduce a new set of large scale, high resolution hydrodynamical simulations of the intergalactic medium: the Sherwood simulation suite. These are performed in volumes 10^3-160^3 h^-3 comoving Mpc^{3}, span almost four orders of magnitude in mass resolution with up to 17.2 billion particles, and employ a variety of physics variations including warm dark matter and galactic outflows. We undertake a detailed comparison of the simulations to high resolution, high signal-to-noise observations of the Lyman-alpha forest over the redshift range 2 < z < 5. The simulations are in very good agreement with the observational data, lending further support to the paradigm that the Lyman-alpha forest is a natural consequence of the web-like distribution of matter arising in LCDM cosmological models. Only a small number of minor discrepancies remain with respect to the observational data. Saturated Lyman-alpha absorption lines with column densities N_HI > 10^14.5 cm^-2 at 2 < z < 2.5 are underpredicted in the models. An uncertain correction for continuum placement bias is required to match the distribution and power spectrum of the transmitted flux, particularly at z > 4. Finally, the temperature of intergalactic gas in the simulations may be slightly too low at z=2.7 and a flatter temperature-density relation is required at z=2.4, consistent with the expected effects of non-equilibrium ionisation during He-II reionisation., Comment: 19 pages, 21 figures, accepted to MNRAS. Images and movies may be viewed at http://www.nottingham.ac.uk/astronomy/sherwood/

Observational implications are derived for two standard models of supernovae-driven galactic winds: a freely expanding steady-state wind and a wind sourced by a self-similarly expanding superbubble including thermal heat conduction. It is shown that, for the steady-state wind, matching the measured correlation between the soft x-ray luminosity and star formation rate of starburst galaxies is equivalent to producing a scaled wind mass-loading factor relative to the star-formation rate of 0.5 - 3, in agreement with the amount inferred from metal absorption line measurements. The match requires the asymptotic wind velocity v_inf to scale with the star formation rate SFR (in solar masses per year) approximately as v_inf ~ (700 - 1000) km/s SFR^{1/6}. The corresponding mass injection rate is close to the amount naturally provided by thermal evaporation from the wall of a superbubble in a galactic disc, suggesting thermal evaporation may be a major source of mass-loading. The predicted mass-loading factors from thermal evaporation within the galactic disc alone, however, are somewhat smaller, 0.2 - 2, so that a further contribution from cloud ablation or evaporation may be required. Both models may account for the 1.4GHz luminosity of unresolved radio sources within starburst galaxies for plausible parameters describing the distribution of relativistic electrons. Further observational tests to distinguish the models are suggested., Comment: 16 pages, 8 figures; modified version of submission to MNRAS

We present the largest homogeneous survey of $z>4.4$ damped Lyman-$\alpha$ systems (DLAs) using the spectra of 163 QSOs that comprise the Giant Gemini GMOS (GGG) survey. With this survey we make the most precise high-redshift measurement of the cosmological mass density of neutral hydrogen, $\Omega_{\rm HI}$. At such high redshift important systematic uncertainties in the identification of DLAs are produced by strong intergalactic medium absorption and QSO continuum placement. These can cause spurious DLA detections, result in real DLAs being missed, or bias the inferred DLA column density distribution. We correct for these effects using a combination of mock and higher-resolution spectra, and show that for the GGG DLA sample the uncertainties introduced are smaller than the statistical errors on $\Omega_{\rm HI}$. We find $\Omega_{\rm HI}=0.98^{+0.20}_{-0.18}\times10^{-3}$ at $\langle z\rangle=4.9$, assuming a 20% contribution from lower column density systems below the DLA threshold. By comparing to literature measurements at lower redshifts, we show that $\Omega_{\rm HI}$ can be described by the functional form $\Omega_{\rm HI}(z)\propto(1+z)^{0.4}$. This gradual decrease from $z=5$ to $0$ is consistent with the bulk of HI gas being a transitory phase fuelling star formation, which is continually replenished by more highly-ionized gas from the intergalactic medium, and from recycled galactic winds., Comment: Accepted by MNRAS. Comments and reference suggestions are still welcome. Data and code for the paper will appear at https://github.com/nhmc/GGG_DLA after the final version has been published

We perform cosmological simulations of the intergalactic medium (IGM) at redshift z ~ 3 using the numerical gravity-hydrodynamics codes GADGET-3 and Enzo for the purpose of modelling the gaseous environments of galaxies. We identify haloes in the simulations using three different algorithms. Different rank orderings of the haloes by mass result, introducing a limiting factor in identifying haloes with observed galaxies. We also compare the physical properties of the gas between the two codes, focussing primarily on the gas outside the virial radius, motivated by recent HI absorption measurements of the gas around z ~ 2 - 3 galaxies. The internal dispersion velocities of the gas in the haloes have converged for a box size of 30 comoving Mpc, but the centre-of-mass peculiar velocities of the haloes have not up to a box size of 60 comoving Mpc. The density and temperature of the gas within the instantaneous turn-around radii of the haloes are adequately captured for box sizes 30 Mpc on a side, but the results are highly sensitive to the treatment of unresolved, rapidly cooling gas, with the gas mass fraction within the virial radius severely depleted by star formation in the GADGET-3 simulations. Convergence of the gas peculiar velocity field on large scales requires a box size of at least 60 Mpc. Outside the turn-around radius, the physical state of the gas agrees to 30 percent or better both with box size and between simulation methods. We conclude that generic IGM simulations make accurate predictions for the intergalactic gas properties beyond the halo turn-around radii, but the gas properties on smaller scales are highly dependent on star formation and feedback implementations., Comment: 16 pages. The definitive version of this article has been accepted for publication in MNRAS, published by Oxford University Press

We study the statistics of the Lyman-$\alpha$ forest in a flat LCDM cosmology with the N-body + Eulerian hydrodynamics code Nyx. We produce a suite of simulations, covering the observationally relevant redshift range $2 \leq z \leq 4$. We find that a grid resolution of 20 kpc/h is required to produce one percent convergence of Lyman-$\alpha$ flux statistics, up to k = 10 h/Mpc. In addition to establishing resolution requirements, we study the effects of missing modes in these simulations, and find that box sizes of L > 40 Mpc/h are needed to suppress numerical errors to a sub-percent level. Our optically-thin simulations with the ionizing background prescription of Haardt & Madau (2012) reproduce an IGM equation of state with $T_0 \approx 10^4 K$ and $\gamma \approx 1.55$ at z=2, with a mean transmitted flux close to the observed values. When using the ionizing background prescription of Faucher-Giguere et al. (2009), the mean flux is 10-15 per cent below observed values at z=2, and a factor of 2 too small at z = 4. We show the effects of the common practice of rescaling optical depths to the observed mean flux and how it affects convergence rates. We also investigate the common practice of `splicing' results from a number of different simulations to estimate the 1D flux power spectrum and show it is accurate at the 10 percent level. Finally, we find that collisional heating of the gas from dark matter particles is negligible in modern cosmological simulations., Comment: 28 pages, 31 figures; version as accepted for MNRAS publication on November 7, 2014

We have obtained spectra of 163 quasars at $z_\mathrm{em}>4.4$ with the Gemini Multi Object Spectrometers on the Gemini North and South telescopes, the largest publicly available sample of high-quality, low-resolution spectra at these redshifts. From this homogeneous data set, we generated stacked quasar spectra in three redshift intervals at $z\sim 5$. We have modelled the flux below the rest-frame Lyman limit ($\lambda_\mathrm{r}<912$\AA) to assess the mean free path $\lambda_\mathrm{mfp}^{912}$ of the intergalactic medium to HI-ionizing radiation. At mean redshifts $z_\mathrm{q}=4.56$, 4.86 and 5.16, we measure $\lambda_\mathrm{mfp}^{912}=(22.2\pm 2.3, 15.1\pm 1.8, 10.3\pm 1.6)h_{70}^{-1}$ proper Mpc with uncertainties dominated by sample variance. Combining our results with $\lambda_\mathrm{mfp}^{912}$ measurements from lower redshifts, the data are well modelled by a simple power-law $\lambda_\mathrm{mfp}^{912}=A[(1+z)/5]^\eta$ with $A=(37\pm 2)h_{70}^{-1}$ Mpc and $\eta = -5.4\pm 0.4$ between $z=2.3$ and $z=5.5$. This rapid evolution requires a physical mechanism -- beyond cosmological expansion -- which reduces the cosmic effective Lyman limit opacity. We speculate that the majority of HI Lyman limit opacity manifests in gas outside galactic dark matter haloes, tracing large-scale structures (e.g. filaments) whose average density (and consequently neutral fraction) decreases with cosmic time. Our measurements of the strongly redshift-dependent mean free path shortly after the completion of HI reionization serve as a valuable boundary condition for numerical models thereof. Having measured $\lambda_\mathrm{mfp}^{912}\approx 10$ Mpc at $z=5.2$, we confirm that the intergalactic medium is highly ionized by that epoch and that the redshift evolution of the mean free path does not show a break that would indicate a recent end to HI reionization., Comment: 16 pages, 11 figures, plus 20 pages of online material; submitted to MNRAS

The sources which reionized the Intergalactic Medium by redshift ~6 are still unknown. A severe constraint on the ionization process is the low emissivity required to maintain the ionization in the Lyman-{\alpha} forest. Simulation-calibrated observations suggest a production rate of at most only a few photons per baryon. In this work, we present a new solution to this "photon-starvation" problem using a weak background of cosmic magnetic fields, which may be present as a consequence of early-Universe physics and subsequent magneto-hydrodynamical amplification. If present, such magnetic fields can induce density perturbations which are dominant on scales comparable to those probed by measurements of hydrogen-absorption lines at redshifts z~2-5. We show that a sub-nanoGauss magnetic field, coherent on scale ~1 Mpc with an almost scale-invariant spectrum, is sufficient to produce significant impact on the effective optical depth, the appearance of the Lyman-{\alpha} forest on quasar spectra, the pixel-flux statistics and the power spectrum of transmitted flux. We also show that such magnetic-field signatures are effectively erased when the metagalactic photoionization rate is increased, hence relaxing the constraint on the cosmic photon budget available for reionization., Comment: 8 pages. Accepted by MNRAS

The first primitive galaxies formed from accretion and mergers by z ~ 15, and were primarily responsible for cosmological reionization and the chemical enrichment of the early cosmos. But a few of these galaxies may have formed in the presence of strong Lyman-Werner UV fluxes that sterilized them of H_2, preventing them from forming stars or expelling heavy elements into the IGM prior to assembly. At masses of 10^8 Ms and virial temperatures of 10^4 K, these halos began to rapidly cool by atomic lines, perhaps forming 10^4 - 10^6 Ms Pop III stars and, later, the seeds of supermassive black holes. We have modeled the explosion of a supermassive Pop III star in the dense core of a line-cooled protogalaxy with the ZEUS-MP code. We find that the supernova (SN) expands to a radius of ~ 1 kpc, briefly engulfing the entire galaxy, but then collapses back into the potential well of the dark matter. Fallback fully mixes the interior of the protogalaxy with metals, igniting a violent starburst and fueling the rapid growth of a massive black hole at its center. The starburst would populate the protogalaxy with stars in greater numbers and at higher metallicities than in more slowly-evolving, nearby halos. The SN remnant becomes a strong synchrotron source that can be observed with eVLA and eMERLIN and has a unique signature that easily distinguishes it from less energetic SN remnants. Such explosions, and their attendant starbursts, may well have marked the birthplaces of supermassive black holes on the sky., Comment: 11 pages, 10 figures, accepted for publication in ApJ

The Square Kilometre Array (SKA) will have a low frequency component (SKA-low) which has as one of its main science goals the study of the redshifted 21cm line from the earliest phases of star and galaxy formation in the Universe. This 21cm signal provides a new and unique window on both the formation of the first stars and accreting black holes and the later period of substantial ionization of the intergalactic medium. The signal will teach us fundamental new things about the earliest phases of structure formation, cosmology and even has the potential to lead to the discovery of new physical phenomena. Here we present a white paper with an overview of the science questions that SKA-low can address, how we plan to tackle these questions and what this implies for the basic design of the telescope., Comment: Accepted for publication in Experimental Astronomy, reformatted to 57 pages, some updated and improved figures and minor changes and updates to the text

Primordial stars are key to primeval structure formation as the first stellar components of primeval galaxies, the sources of cosmic chemical enrichment and likely cosmic reionization, and they possibly gave rise to the supermassive black holes residing at the centres of galaxies today. While the direct detection of individual Pop III stars will likely remain beyond reach for decades to come, we show their supernova remnants may soon be detectable in the radio. We calculate radio synchrotron signatures between 0.5 - 35 GHz from hydrodynamical computations of the supernova remnants of Pop III stars in minihaloes. We find that hypernovae yield the brightest systems, with observed radio fluxes as high as 1 - 10 muJy. Less energetic Type II supernovae yield remnants about a factor of 30 dimmer and pair-instability supernova remnants are dimmer by a factor of more than 10,000. Because of the high gas densities of the progenitor environments, synchrotron losses severely limit the maximum emission frequencies, producing a distinctive peaked radio spectrum distinguishable from normal galactic supernova remnant spectra. Hypernovae radio remnants should be detectable by existing radio facilities like eVLA and eMERLIN while Type II supernova remnants will require the Square Kilometre Array. The number counts of hypernova remnants at z > 20 with fluxes above 1 muJy are expected to be one per hundred square degree field, increasing to a few per square degree if they form down to z = 10. The detection of a z > 20 Type II supernova remnant brighter than 1 nJy would require a 100 - 200 square degree field, although only a 1 - 2 square degree field for those forming down to z = 10. Hypernova and Type II supernova remnants are easily separated from one another by their light curves, which will enable future surveys to use them to constrain the initial mass function of Pop III stars., Comment: 12 pages, 9 figures; major revision; to appear in MNRAS

Two methods are developed for solving the steady-state spherically symmetric radiative transfer equation for resonance line radiation emitted by a point source in the Intergalactic Medium. One method is based on solving the ray and moment equations using finite differences. The second uses a Monte Carlo approach incorporating methods that greatly improve the accuracy compared with previous approaches in this context. Several applications are presented serving as test problems for both a static medium and an expanding medium, including inhomogeneities in the density and velocity fields. Solutions are obtained in the coherent scattering limit and for Doppler RII redistribution with and without recoils. We find generally that the radiation intensity is linear in the cosine of the azimuthal angle with respect to radius to high accuracy over a broad frequency region across the line centre for both linear and perturbed velocity fields, yielding the Eddington factors f(nu) = 1/3 and g(nu) = 3/5. We show the radiation field produced by a point source divides into three spatial regimes for a uniformly expanding homogeneous medium: at radii r small compared with a characteristic radius r*, the mean intensity near line centre varies as 1/ r^(7/3), while at r > r* it approaches 1/ r^2; for r << r* it is modified by frequency redistribution. Before the reionization epoch, r* takes on the universal value 1.1 Mpc, independent of redshift. The mean intensity and scattering rate are found to be very sensitive to the gradient of the velocity field, growing exponentially with the amplitude of the perturbation as the limit of a vanishing velocity gradient is approached near the source. We expect the 21cm signal from the Epoch of Reionization to thus be a sensitive probe of both the density and the peculiar velocity fields., Comment: 27 pages, 26 figures, 10 supplementary tables; submitted to MNRAS

The full reionization of intergalactic helium was a major event in the history of the IGM, and UV observations of the He II Gunn-Peterson trough allow us to characterize the end of this process at z~3. Due to intervening hydrogen absorption, quasars allowing such study are rare, with only 33 known in the literature, and most of those are very recent discoveries. We expand on our previous discovery work, and present 13 new He II quasars with redshifts 2.82 < z < 3.77, here selected with ~80% efficiency, and including several that are much brighter than the vast majority of those previously known. This is the largest sample of uniformly observed He II quasars covering such a broad redshift range, and they show evidence of IGM opacity increasing with redshift, as expected for the helium reionization epoch. No evidence of He II Ly{\alpha} quasar emission is seen in individual or averaged spectra, posing a problem for standard models of the broad line region. The current rapid advance in the study of He II quasars has been greatly facilitated by the Cosmic Origins Spectrograph on HST, and we discuss the instrumental and other subtleties that must be taken into account in IGM He II observations., Comment: AJ accepted; 14 pages, 7 figures

The first major star-forming galaxies and Active Galactic Nuclei will produce Balmer and higher order extended haloes during the Epoch of Reionization through the scattering of Lyman resonance line photons off the surrounding neutral intergalactic gas. The optical depth dependence of the scattering rates will produce a signal sensitive to both the density and velocity fluctuations of the gas, offering the possibility of probing the ionization region and flow field surrounding young star-forming galaxies. The requirements for detecting the haloes in the infra-red using a space-based telescope are discussed, along with an assessment of the possibility of detecting the haloes using the Tunable Filter Imager on the James Webb Space Telescope., Comment: 7 pages, 10 figures. Submitted to MNRAS

Observations of He II Ly{\alpha} Gunn-Peterson troughs have proved to be a valuable probe of the epoch of helium reionization at z~3. Since this optical depth can become unmeasurably large even for modest He II fractions, various alternate techniques have been proposed to push to higher redshift, and among the more promising is looking at higher order Lyman-series troughs. We here report four new observations of the He II Ly{\beta} trough, including new data on the only sightline with a prior Ly{\beta} observation. However, the effective optical depth ratio {\tau}_eff,{\beta}/{\tau}_eff,{\alpha} is not simply predicted by (f_{\beta} {\lambda}_{\beta})/(f_{\alpha} {\lambda}_{\alpha})=0.16, and we analyze cosmological simulations to find that the correct ratio for helium at z~3 is ~0.35. In one case we infer {\tau}_eff,{\alpha} > 8.8, strong evidence that helium was not fully reionized at z=3.2--3.5, in agreement with previous measurements suggesting a later completion of reionization., Comment: ApJ accepted. 25 pages, 3 figures, 4 tables

IGMtransmission is a Java graphical user interface that implements Monte Carlo simulations to compute the corrections to colours of high-redshift galaxies due to intergalactic attenuation based on current models of the Intergalactic Medium. The effects of absorption due to neutral hydrogen are considered, with particular attention to the stochastic effects of Lyman Limit Systems. Attenuation curves are produced, as well as colours for a wide range of filter responses and model galaxy spectra. Alternative filter response curves and spectra may be readily uploaded. The code is freely available from http://code.google.com/p/igmtransmission. It is licensed under the GNU General Public License v.3., Comment: 13 pages, 6 figure, user manual for IGMtransmission

A unified description is provided for the 21cm signatures arising from minihaloes against a bright background radio source and against the Cosmic Microwave Background (CMB), within the context of a dynamical collapsing cosmological spherical halo model. The equivalent width distribution of the resulting 21cm forest is computed for LCDM cosmologies, along with the brightness temperature differential relative to the CMB. The effects of an ambient Ly-alpha radiation field and heating of the IGM on the signatures are included. It is shown that the dynamical effects of heating substantially suppress absorption features in the 21cm forest with observed equivalent widths exceeding 0.15 kHz. It is demonstrated how measurements of excess fluctuations beyond detector noise could make a statistical detection of the weaker absorption features against a bright background radio source. It is also shown that a Ly-alpha radiation field only a few percent the thermalisation rate is sufficient to render the minihalo signal against the CMB negligible compared with the signal from the diffuse IGM component. The 21cm signals are found to be very sensitive to the amount of small scale power in the primordial density fluctuation spectrum. The effects of gas cooling via radiative atomic and molecular processes and of star formation on setting the maximum mass of the minihaloes giving rise to a 21cm signal are included, with allowance made for the suppression of molecular hydrogen formation by an ambient UV radiation field., Comment: Substantial revision: paper restructured; hydrodynamical model with heating included; discussion of statistical detection of absorption fluctuations from 21cm forest added. 34 pages; 34 figures. Definitive version published in Monthly Notices

Quasars that allow the study of IGM He II are very rare, since they must be at high redshift along sightlines free of substantial hydrogen absorption, but recent work has dramatically expanded the number of such quasars known. We analyze two dozen higher-redshift (z=3.1-3.9) low-resolution He II quasar spectra from HST and find that their He II Gunn-Peterson troughs suggest exclusion of very early and very late reionization models, favoring a reionization redshift of z~3. Although the data quality is not sufficient to reveal details such as the expected redshift evolution of helium opacity, we obtain the first ensemble measure of helium opacity at high redshift averaged over many sightlines: tau=4.90 at z~3.3. We also find that it would be very difficult to observe the IGM red wing of absorption from the beginning of He II reionization, but depending on the redshift of reionization and the size of ionization zones, it might be possible to do so in some objects with the current generation of UV spectrographs., Comment: ApJ accepted. 9 pages, 4 figures

We examine the temperature structure of the intergalactic medium IGM) surounding a hard radiation source, such as a Quasi-Stellar Object (QSO), as it responds to the onset of helium reionization by the source. We model the reionization using a radiative transfer (RT) code coupled to a particle-mesh (PM) N-body code. Neutral hydrogen and helium are initially ionized by a starburst spectrum, which is allowed to gradually evolve into a power law spectrum (fnu ~ nu^(-0.5)). Multiple simulations were performed with different times for the onset and dominance of the hard spectrum, with onset redshifts ranging from z = 3.5 to 5.5. The source is placed in a high-density region to mimic the expected local environment of a QSO. Simulations with the source placed in a low-density environment were also performed as control cases to explore the role of the environment on the properties of the surrounding IGM. We find in both cases that the IGM temperature within the HeIII region produced exceeds the IGM temperature before full helium reionization, resulting in a "thermal proximity effect", but that the temperature in the HeIII region increases systematically with distance from the source. With time the temperature relaxes with a reduced spread as a function of impact parameter along neighbouring lines of sight, although the trend continues to persist until z = 2. Such a trend could be detected using the widths of intervening metal absorption systems using high resolution, high signal-to-noise ratio spectra., Comment: 17 pages, 12 figures, for publication in MNRAS

Absorption along quasar sightlines remains among the most sensitive direct measures of HeII reionization in much of the intergalactic medium (IGM). Until recently, fewer than a half-dozen unobscured quasar sightlines suitable for the HeII Gunn-Peterson test were known; although these handful demonstrated great promise, the small sample size limited confidence in cosmological inferences. We have recently added nine more such clean HeII quasars, exploiting SDSS quasar samples, broadband UV imaging from GALEX, and high-yield UV spectroscopic confirmations from HST. Here we markedly expand this approach by cross-correlating SDSS DR7 and GALEX GR4+5 to catalog 428 SDSS and 165 other quasars with z>2.78 having likely (~70%) GALEX detections, suggesting they are bright into the far-UV. Reconnaissance HST Cycle 16 Supplemental prism data for 29 of these new quasar-GALEX matches spectroscopically confirm 17 as indeed far-UV bright. At least 10 of these confirmations have clean sightlines all the way down to HeII Lyman-alpha, substantially expanding the number of known clean HeII quasars, and reaffirming the order of magnitude enhanced efficiency of our selection technique. Combined confirmations from this and our past programs yield more than twenty HeII quasars, quintupling the sample. These provide substantial progress toward a sample of HeII quasar sightlines large enough, and spanning a sufficient redshift range, to enable statistical IGM studies that may avoid individual object peculiarity and sightline variance. Our expanded catalog of hundreds of high-likelihood far-UV-bright QSOs additionally will be useful for understanding the extreme-UV properties of the quasars themselves., Comment: 32 pages, 6 figures, 3 tables; accepted by ApJS

The role of higher order Lyman series photons on the 21cm absorption or emission signature of the IGM against the background CMB during the Epoch of Reionisation is examined. It is shown that, taking into account the diminishing resonance line scattering cross section with increasing Lyman order, a non-negligible net scattering rate of higher order Lyman photons is expected. The resulting radiative cascades will substantially enhance the number density of Lyman-alpha photons near a radiation source. It is also shown that the higher order Lyman series photons are able to collisionally heat the IGM by amounts of tens to hundreds of degrees kelvin. The possibility that the Wouthuysen-Field effect may be suppressed by the presence of dust near a galaxy is discussed, and it is shown that the higher order Lyman series photons would still induce the effect, but with a somewhat reduced 21cm radiation efficiency. It is also demonstrated that extended low surface brightness emission line halos will be produced from radiative cascades following the scattering of higher order Lyman series photons. These halos would provide a unique means of confirming that reionisation source candidates were surrounded by an IGM that was still largely neutral on large scales., Comment: 16 pages, 6 figures; submitted to MNRAS

The spectroscopic Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) galaxy sample represents the final set of galaxies observed using the original SDSS target selection criteria. We analyse the clustering of galaxies within this sample, including both the Luminous Red Galaxy (LRG) and Main samples, and also include the 2-degree Field Galaxy Redshift Survey (2dFGRS) data. Baryon Acoustic Oscillations are observed in power spectra measured for different slices in redshift; this allows us to constrain the distance--redshift relation at multiple epochs. We achieve a distance measure at redshift z=0.275, of r_s(z_d)/D_V(0.275)=0.1390+/-0.0037 (2.7% accuracy), where r_s(z_d) is the comoving sound horizon at the baryon drag epoch, D_V(z)=[(1+z)^2D_A^2cz/H(z)]^(1/3), D_A(z) is the angular diameter distance and H(z) is the Hubble parameter. We find an almost independent constraint on the ratio of distances D_V(0.35)/D_V(0.2)=1.736+/-0.065, which is consistent at the 1.1sigma level with the best fit Lambda-CDM model obtained when combining our z=0.275 distance constraint with the WMAP 5-year data. The offset is similar to that found in previous analyses of the SDSS DR5 sample, but the discrepancy is now of lower significance, a change caused by a revised error analysis and a change in the methodology adopted, as well as the addition of more data. Using WMAP5 constraints on Omega_bh^2 and Omega_ch^2, and combining our BAO distance measurements with those from the Union Supernova sample, places a tight constraint on Omega_m=0.286+/-0.018 and H_0 = 68.2+/-2.2km/s/Mpc that is robust to allowing curvature and non-Lambda dark energy. This result is independent of the behaviour of dark energy at redshifts greater than those probed by the BAO and supernova measurements. (abridged), Comment: 22 pages, 16 figures, minor changes to match version published in MNRAS

We present the power spectrum of the reconstructed halo density field derived from a sample of Luminous Red Galaxies (LRGs) from the Sloan Digital Sky Survey Seventh Data Release (DR7). The halo power spectrum has a direct connection to the underlying dark matter power for k <= 0.2 h/Mpc, well into the quasi-linear regime. This enables us to use a factor of ~8 more modes in the cosmological analysis than an analysis with kmax = 0.1 h/Mpc, as was adopted in the SDSS team analysis of the DR4 LRG sample (Tegmark et al. 2006). The observed halo power spectrum for 0.02 < k < 0.2 h/Mpc is well-fit by our model: chi^2 = 39.6 for 40 degrees of freedom for the best fit LCDM model. We find \Omega_m h^2 * (n_s/0.96)^0.13 = 0.141^{+0.009}_{-0.012} for a power law primordial power spectrum with spectral index n_s and \Omega_b h^2 = 0.02265 fixed, consistent with CMB measurements. The halo power spectrum also constrains the ratio of the comoving sound horizon at the baryon-drag epoch to an effective distance to z=0.35: r_s/D_V(0.35) = 0.1097^{+0.0039}_{-0.0042}. Combining the halo power spectrum measurement with the WMAP 5 year results, for the flat LCDM model we find \Omega_m = 0.289 +/- 0.019 and H_0 = 69.4 +/- 1.6 km/s/Mpc. Allowing for massive neutrinos in LCDM, we find \sum m_{\nu} < 0.62 eV at the 95% confidence level. If we instead consider the effective number of relativistic species Neff as a free parameter, we find Neff = 4.8^{+1.8}_{-1.7}. Combining also with the Kowalski et al. (2008) supernova sample, we find \Omega_{tot} = 1.011 +/- 0.009 and w = -0.99 +/- 0.11 for an open cosmology with constant dark energy equation of state w., Comment: 26 pages, 19 figures, submitted to MNRAS. The power spectrum and a module to calculate the likelihoods is publicly available at http://lambda.gsfc.nasa.gov/toolbox/lrgdr/ . v2 fixes abstract formatting issue

We show that, due to the high optical depth of the intergalactic medium to Lyman-alpha photons before the Epoch of Reionization, the Lyman-alpha scattering rate responsible for the Wouthuysen-Field effect from an isolated source will be negligible unless (1) there is sufficient time for the scattering photons to establish a steady state, or (2) the scattering gas is undergoing internal expansion or has a peculiar motion of tens to hundreds of km/s away from the source. We present steady-state solutions in the radiative diffusion approximation for the radiation field trapped in a clump of gas and show that this may result in an enhancement, by a factor of up to 10^6, of the strength of the Wouthuysen-Field effect over that obtained from the free-streaming limit. Solutions to the time-dependent diffusion equation, however, suggest that the timescales required to reach such a steady state will generally exceed the source lifetimes. In the presence of internal expansion, a steady state may be established as photons are redshifted into the red wing, and significant enhancement in the scattering rate may again be produced. Alternatively, a substantial scattering rate may arise in systems with a peculiar motion away from the source that redshifts the received radiation into the resonance line centre. As a consequence, at epochs z<30, when collisional decoupling is small except in dense regions, and prior to the establishment of any large-scale diffuse radiation field of resonance line photons, the 21cm signature from the Intergalactic Medium produced by the Wouthuysen-Field effect will in general trace the peculiar velocity field of the gas in addition to its density structure., Comment: 11 pages, 7 figures. Accepted for publication in MNRAS

Investigations of He II Ly-alpha (304 A rest) absorption toward a half-dozen quasars at z~3-4 have demonstrated the great potential of helium studies of the IGM, but the current critically small sample size of clean sightlines for the He II Gunn-Peterson test limits confidence in cosmological inferences, and a larger sample is required. Although the unobscured quasar sightlines to high redshift are extremely rare, SDSS DR6 provides thousands of z>2.8 quasars. We have cross-correlated these SDSS quasars with GALEX GR2/GR3 to establish a catalog of 200 higher-confidence (~70% secure) cases of quasars at z=2.8-5.1 potentially having surviving far-UV (restframe) flux. We also catalog another 112 likely far-UV-bright quasars from GALEX cross-correlation with other (non-SDSS) quasar compilations. Reconnaissance UV prism observations with HST of 24 of our SDSS/GALEX candidates confirm 12 as detected in the far-UV, with at least 9 having flux extending to very near the He II break; with refinements our success rate is even higher. Our SDSS/GALEX selection approach is thereby confirmed to be an order of magnitude more efficient than previous He II quasar searches, more than doubles the number of spectroscopically confirmed clean sightlines to high redshift, and provides a resource list of hundreds of high-confidence sightlines for upcoming He II and other far-UV studies from HST. Our reconnaissance HST prism spectra suggest some far-UV diversity, confirming the need to obtain a large sample of independent quasar sightlines across a broad redshift range to assess such issues as the epoch(s) of helium reionization, while averaging over individual-object pathology and/or cosmic variance., Comment: 32 pages, 7 figures, accepted by ApJ

We measure the evolution of the luminous red galaxy (LRG) luminosity function in the redshift range 0.13L*) red galaxies have grown by less than 50% (at 99% confidence), since z=0.9, in stark contrast to the factor of 2-4 growth observed in the L* red galaxy population over the same epoch. We also investigate the evolution of the average LRG spectrum since z~0.9 and find the high-redshift composite to be well-described as a passively evolving example of the composite galaxy observed at low-redshift. From spectral fits to the composite spectra, we find at most 5% of the stellar mass in massive red galaxies may have formed within 1Gyr of z=0.9. While L* red galaxies are clearly assembled at z<1, 3L* galaxies appear to be largely in place and evolve little beyond the passive evolution of their stellar populations over the last half of cosmic history., Comment: 19 pages, 19 figures, 7 tables; accepted for publication in ApJ

Intergalactic space is filled with a pervasive medium of ionized gas, the Intergalactic Medium (IGM). A residual neutral fraction is detected in the spectra of Quasi-Stellar Objects at both low and high redshifts, revealing a highly fluctuating medium with temperatures characteristic of photoionized gas. The statistics of the fluctuations are well-reproduced by numerical gravity-hydrodynamics simulations within the context of standard cosmological structure formation scenarios. As such, the study of the IGM offers an opportunity to probe the nature of the primordial density fluctuations on scales unavailable to other methods. The simulations also suggest the IGM is the dominant reservoir of baryons produced by the Big Bang, and so the principal source of the matter from which galaxies formed. The detection of metal systems within the IGM shows that it was enriched by evolved stars early in its history, demonstrating an intimate connection between galaxy formation and the IGM. The author presents a comprehensive review of the current understanding of the structure and physical properties of the IGM and its relation to galaxies, concluding with comments on prospects for furthering the study of the IGM using future ground-based facilities and space-based experiments., Comment: 69 pages; accepted version to appear in Reviews of Modern Physics; text and equation typos corrected; all figures included

We present a Fourier analysis of the clustering of galaxies in the combined Main galaxy and Luminous Red Galaxy (LRG) Sloan Digital Sky Survey (SDSS) Data Release 5 (DR5) sample. The aim of our analysis is to consider how well we can measure the cosmological matter density using the signature of the horizon at matter-radiation equality embedded in the large-scale power spectrum. The new data constrains the power spectrum on scales 100--600h^-1Mpc with significantly higher precision than previous analyses of just the SDSS Main galaxies, due to our larger sample and the inclusion of the LRGs. This improvement means that we can now reveal a discrepancy between the shape of the measured power and linear CDM models on scales 0.01

We measure the cosmological matter density by observing the positions of baryon acoustic oscillations in the clustering of galaxies in the Sloan Digital Sky Survey (SDSS). We jointly analyse the main galaxies and LRGs in the SDSS DR5 sample, using over half a million galaxies in total. The oscillations are detected with 99.74% confidence (3.0sigma assuming Gaussianity) compared to a smooth power spectrum. When combined with the observed scale of the peaks within the CMB, we find a best-fit value of Omega_m=0.256+0.029-0.024 (68% confidence interval), for a flat Lambda cosmology when marginalising over the Hubble parameter and the baryon density. This value of the matter density is derived from the locations of the baryon oscillations in the galaxy power spectrum and in the CMB, and does not include any information from the overall shape of the power spectra. This is an extremely clean cosmological measurement as the physics of the baryon acoustic oscillation production is well understood, and the positions of the oscillations are expected to be independent of systematics such as galaxy bias., Comment: 5 pages, 3 figures, updated to match version accepted by ApJ

We examine the temperature structure of the IGM due to the passage of individual ionisation fronts using a radiative transfer (RT) code coupled to a particle-mesh (PM) N-body code. Multiple simulations were performed with different spectra of ionising radiation: a power law (goes as nu^{-0.5}), miniquasar, starburst, and a time-varying spectrum that evolves from a starburst spectrum to a power law. The RT is sufficiently resolved in time and space to correctly model both the ionisation state and the temperature across the ionisation front. We find the post-ionisation temperature of the reionised intergalactic medium (IGM) is sensitive to the spectrum of the source of ionising radiation, which may be used to place strong constraints on the nature of the sources of reionisation. Radiative transfer effects also produce large fluctuations in the HeII to HI number density ratio eta. The spread in values is smaller than measured, except for the time-varying spectrum. For this case, the spread evolves as the spectral nature of the ionising background changes. Large values for eta are found in partially ionised HeII as the power-law spectrum begins to dominate the starburst, suggesting that the large eta values measured may be indicating the onset of the HeII reionisation epoch., Comment: Accepted to MNRAS. Version with high resolution colour figures available at http://www.roe.ac.uk/~ert/Publications/Tittley_Meiksin_07.pdf

A formal derivation is presented of the energy transfer rate between radiation and matter due to the scattering of an isotropic distribution of resonant photons. The derivation is developed in the context of the two-level atom in the absence of collisions and radiative transitions to and from the continuum, but includes the full angle-averaged redistribution function for photon scattering. The result is compared with previous derivations, all of which have been based on the Fokker-Planck approximation to the radiative transfer equation. A new Fokker-Planck approximation, including an extension to higher (post-diffusive) orders, is derived to solve the radiative transfer equation, and time-dependent numerical solutions are found. The relaxation of the colour temperature to the matter temperature is computed as the radiation field approaches statistical equilibrium through scattering. The results are discussed in the context of the Wouthuysen-Field mechanism for coupling the 21cm spin temperature of neutral hydrogen to the kinetic temperature of the gas through LyA scattering. The evolution of the heating rate is also computed, and shown to diminish as the gas approaches statistical equilibrium., Comment: 13 pages, 4 figures. Submitted to MNRAS. RT eq. simplified to generalise results including stimulated emission

We determine the number counts and z=0-5 luminosity function for a well-defined, homogeneous sample of quasars from the Sloan Digital Sky Survey (SDSS). We conservatively define the most uniform statistical sample possible, consisting of 15,343 quasars within an effective area of 1622 deg^2 that was derived from a parent sample of 46,420 spectroscopically confirmed broad-line quasars in the 5282 deg^2 of imaging data from SDSS Data Release Three. The sample extends from i=15 to i=19.1 at z<3 and to i=20.2 for z>3. The number counts and luminosity function agree well with the results of the 2dF QSO Survey, but the SDSS data probe to much higher redshifts than does the 2dF sample. The number density of luminous quasars peaks between redshifts 2 and 3, although uncertainties in the selection function in this range do not allow us to determine the peak redshift more precisely. Our best fit model has a flatter bright end slope at high redshift than at low redshift. For z<2.4 the data are best fit by a redshift-independent slope of beta = -3.1 (Phi(L) propto L^beta). Above z=2.4 the slope flattens with redshift to beta=-2.37 at z=5. This slope change, which is significant at a >5-sigma level, must be accounted for in models of the evolution of accretion onto supermassive black holes., Comment: 57 pages, 21 figures (9 color); minor changes to reflect the version accepted by AJ; higher resolution version available at ftp://ftp.astro.princeton.edu/gtr/dr3qlf/Feb1306/

The colours of high redshift Type II QSOs are synthesized from observations of moderate redshift systems. It is shown that Type II QSOs are comparable to starbursts in their success at matching the colours of z_850-dropouts and i_775-drops in the Hubble Ultra Deep Field, and more naturally account for the bluest objects detected. Type II QSOs may also account for some of the i_775-drops detected in the GOODS fields. It is shown that by combining imaging data from the Hubble Space Telescope and the James Webb Space Telescope, it will be possible to clearly separate Type II QSOs from Type I QSOs and starbursts based on their colours. Similarly, it is shown that the UKIDSS ZYJ filters may be used to discriminate high redshift Type II QSOs from other objects. If Type II QSOs are prevalent at high redshifts, then AGN may be major contributors to the re-ionization of the Intergalactic Medium., Comment: 11 pages, 10 figures; to be published in MNRAS; new predictions for corrected UKIDSS UDS limits